4Y2Q: Structure Of Soluble Epoxide Hydrolase In Complex With 1-[3- (trifluoromethyl)pyridin-2-yl]piperazine

Soluble epoxide hydrolase (sEH) is a potential target for the treatment of inflammation and hypertension. X-ray crystallographic fragment screening was used to identify fragment hits and their binding modes. Eight fragment hits were identified via soaking of sEH crystals with fragment cocktails, and the co-crystal structures of these hits were determined via individual soaking. Based on the binding mode, N-ethylmethylamine was identified as a promising scaffold that forms hydrogen bonds with the catalytic residues of sEH, Asp335, Tyr383, and Tyr466. Compounds containing this scaffold were selected from an in-house chemical library and assayed. Although the starting fragment had a weak inhibitory activity (IC50: 800muM), we identified potent inhibitors including 2-({[2-(adamantan-1-yl)ethyl]amino}methyl)phenol exhibiting the highest inhibitory activity (IC50: 0.51muM). This corresponded to a more than 1500-fold increase in inhibitory activity compared to the starting fragment. Co-crystal structures of the hit compounds demonstrate that the binding of N-ethylmethylamine to catalytic residues is similar to that of the starting fragment. We therefore consider crystallographic fragment screening to be appropriate for the identification of weak but promising fragment hits.
PDB ID: 4Y2QDownload
MMDB ID: 129124
PDB Deposition Date: 2015/2/10
Updated in MMDB: 2015/05
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Source Organism:
Similar Structures:
Biological Unit for 4Y2Q: dimeric; determined by author and by software (PISA)
Molecular Components in 4Y2Q
Label Count Molecule
Proteins (2 molecules)
Bifunctional Epoxide Hydrolase 2(Gene symbol: EPHX2)
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

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